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Table 1 Retrotransposons that integrate adjacent to tRNA genes

From: Retrotransposon targeting to RNA polymerase III-transcribed genes

Mobile element Clade Hosta Preferred integration site Host factors mediating this insertion preference
LTR Retrotransposons
Ty1 Ty1-copia Saccharomyces cerevisiae ~ 1 kb window upstream of RNA Pol III-transcribed genes, including tRNA and 5S rRNA genes [13, 14, 21] Ty1-IN interaction with Rpc40 [29] and Ty1-IN interaction with Rpc53, Rpc34, Rpc31 [30]
Ty2 Ty1-copia Saccharomyces cerevisiae ~ 1 kb window upstream of RNA Pol III-transcribed genes [21]  
Ty3 Ty3-gypsy Saccharomyces cerevisiae 1–4 bp upstream of tRNA TSSb [93] Ty3-IN interaction with TFIIIB [88, 89]
Ty3p Ty3-gypsy Saccharomyces paradoxus ~ 6 bp upstream of tRNA TSS [110]  
Ty4 Ty1-copia Saccharomyces cerevisiae ~ 1 kb window upstream of RNA Pol III-transcribed genes [21]  
Tj1 Ty3-gypsy Schizosaccharomyces japonicus 1–10 bp upstream of tRNA TSS [121]  
Beta/Tca8 Ty3-gypsy Candida albicans 6-30 bp upstream of tRNA MCSc [119]  
Tyl3 Ty3-gypsy Yarrowia lipolytica ~ 5 bp upstream of tRNA TSS [116]  
Ylt1 Ty3-gypsy Yarrowia lipolytica ~ 5 bp upstream of tRNA TSS [117]  
Tyl6 Ty3-gypsy Yarrowia lipolytica ~ 5 bp upstream of tRNA TSS [115]  
DGLT-A Ty3-gypsy Dictyostelium discoideum 13–33 bp upstream of tRNA MCS [125]  
Skipper-2 Ty3-gypsy Dictyostelium discoideum 8–23 bp downstream of tRNA gene [124, 172]  
Non-LTR Retrotransposons
TRE5 L1 Dictyostelium discoideum 40–54 bp upstream of tRNA MCS; 37–41 bp upstream of extrachromosomal 5S rRNA genes [125, 134, 135, 174] TRE5 ORF1 interaction with TFIIIB [132]
TRE3 L1 Dictyostelium discoideum 40–150 bp downstream tRNA genes [137, 175]  
NLTR-A L1 Dictyostelium purpureum 2–6 bp upstream of tRNA MCS [124]  
NLTR-B L1 Polysphondylium pallidum 39–64 bp upstream of tRNA MCS [124]  
  1. aHost that retrotransposon was first identified in
  2. bTSS refers to the tRNA transcription start site which is ~ 10 bp upstream of the mature tRNA
  3. cMCS refers to the tRNA mature coding sequence